[R] sresid with lme4
Hi all, does anyone know how to extract or calculate studentized residuals for mixed effects models estimated with the lme4 package? kind regards, Rense -- View this message in context: http://r.789695.n4.nabble.com/sresid-with-lme4-tp4305922p4305922.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] warning inside loop
Dear William,
thank you kindly for this solution: it provides exactly what I need,
especially due to the fact that the encapsulating function returns a list,
from which I can extract all the information I need.
kind regards,
Rense Nieuwenhuis
William Dunlap wrote:
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Rense
Sent: Monday, January 11, 2010 3:07 PM
To: r-help@r-project.org
Subject: [R] warning inside loop
Hi,
I'm running some data simulations using (mixed effects)*
regression models
that show difficulty to converge. Therefore, I seek a way of capturing
warnings (of false convergence) inside a loop.
Inside that loop, I modify data and estimate a model. I do so
many times
with slightly different modifications of the data. Next, I
extract some of
the model parameters and store these in a matrix. However, as
some of the
models do not converge well, some of the stored parameters
are extracted
from the ill-converged models. Therefore, I seek a way of
automatically
detecting whether the estimation procedure has resulted in a
warning, so I
can distinguish between the well- and ill-converged models.
I have been trying to use functions as warnings(), as well as
using the
object last.warning, but unfortunately to no avail.
Try withCallingHandlers(), as in the following function
with returns the value of the expression along with
any warning messages as a list:
withWarnings
function (expr)
{
warnings - character()
retval - withCallingHandlers(expr, warning = function(ex) {
warnings - c(warnings, conditionMessage(ex))
invokeRestart(muffleWarning)
})
list(Value = retval, Warnings = warnings)
}
environment: R_GlobalEnv
Typical usage would be:
lapply(-1:1, function(i)withWarnings(log(i)))
[[1]]
[[1]]$Value
[1] NaN
[[1]]$Warnings
[1] NaNs produced
[[2]]
[[2]]$Value
[1] -Inf
[[2]]$Warnings
character(0)
[[3]]
[[3]]$Value
[1] 0
[[3]]$Warnings
character(0)
Perhaps there is some encapsulation of this already in some
package, as try() encapsulates error catching.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
Although I cannot provide a reproducible example, I
schematically represent
the procedure I seek to use below:
for (i in 1:10)
{
modify data
estimate model
evaluate whether estimation produced warning
extract model parameters, and store whether warning occured
}
I hope any one can give some guidelines on how to deal with
warnings inside
a loop.
With Kind regards,
Rense
*Although I use the lme4 package for that actual analysis, I sent my
question to this mailinglist (instead of the R mixed list)
because I believe
this is a general issue, rather than one associated
exclusively with mixed
models.
--
View this message in context:
http://n4.nabble.com/warning-inside-loop-tp1011667p1011667.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://n4.nabble.com/warning-inside-loop-tp1011667p1011979.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] warning inside loop
Hi,
I'm running some data simulations using (mixed effects)* regression models
that show difficulty to converge. Therefore, I seek a way of capturing
warnings (of false convergence) inside a loop.
Inside that loop, I modify data and estimate a model. I do so many times
with slightly different modifications of the data. Next, I extract some of
the model parameters and store these in a matrix. However, as some of the
models do not converge well, some of the stored parameters are extracted
from the ill-converged models. Therefore, I seek a way of automatically
detecting whether the estimation procedure has resulted in a warning, so I
can distinguish between the well- and ill-converged models.
I have been trying to use functions as warnings(), as well as using the
object last.warning, but unfortunately to no avail.
Although I cannot provide a reproducible example, I schematically represent
the procedure I seek to use below:
for (i in 1:10)
{
modify data
estimate model
evaluate whether estimation produced warning
extract model parameters, and store whether warning occured
}
I hope any one can give some guidelines on how to deal with warnings inside
a loop.
With Kind regards,
Rense
*Although I use the lme4 package for that actual analysis, I sent my
question to this mailinglist (instead of the R mixed list) because I believe
this is a general issue, rather than one associated exclusively with mixed
models.
--
View this message in context:
http://n4.nabble.com/warning-inside-loop-tp1011667p1011667.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Time-travelling laptop, or problem with system.time?
Playing around with my new laptop (Macbook, 2.4Ghz), I encountered unexplained timings using system.time. I did the following: X - Matrix(rnorm(1e6), 1000) system.time(for(i in 1:25) X%*%X) user system elapsed 8.306 0.591 5.031 system.time(for(i in 1:25) solve(X)) user system elapsed 8.933 1.331 6.684 system.time(for(i in 1:10) svd(X)) user system elapsed 36.989 3.665 33.384 From R-News I got the following description: The returned value consists of user time (CPU time R needs for calculations), system time (time the system is using for processing requests, e.g., for handling files), total time (how long it really took to process the command) and — depending on the operating system in use — two further elements. Do I misunderstand these timings, or is my laptop indeed capable of time travel? Kind regards, Rense -- View this message in context: http://www.nabble.com/Time-travelling-laptop%2C-or-problem-with-system.time--tp20279832p20279832.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Importing data
Hi, you might try to use the foreign-package, which contains the function read.spss. This works fine most of the time, For a description of its usage, see the help-files or my own website: http://www.rensenieuwenhuis.nl/r-project/manual/basics/getting-data- into-r-2/ Remember, you'll need to install the foreign-package first. Hope this helps, Rense Nieuwenhuis On Jan 6, 2008, at 12:46 , Simo Vundla wrote: Hi, I'm trying to import categorical data from SPSS to R using the script: xxx -spss.get(xxx.por, use.value.labels=TRUE) but unfortunately am getting an error message 'error reading portable-file dictionary'. I have successfully imported data in the past. What could be the problem with this data? Thanks Simo __ __ Be a better friend, newshound, and [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame manipulation - newbie question
Hi, you may want to use that apply / tapply function. Some find it a bit hard to grasp at first, but it will help you many times in many situations when you get the hang of it. Maybe you can get some information on my site: http:// www.rensenieuwenhuis.nl/r-project/manual/basics/tables/ Hope this helps, Rense Nieuwenhuis On Jan 3, 2008, at 11:53 , José Augusto M. de Andrade Junior wrote: Hi all, Could someone please explain how can i efficientily query a data frame with several factors, as shown below: -- --- Data frame: pt.knn -- --- row | k.idx | step.forwd | pt.num | model | prev | value | abs.error 1 2000 1 lm 09 10.5 1.5 2 2000 2 lm 11 10.5 1.5 3 2011 1 lm 10 12 2.0 4 2011 2 lm 12 12 2.0 5 2022 1 lm 12 12.1 0.1 6 2022 2 lm 12 12.1 0.1 7 2000 1 rlm 10.1 10.5 0.4 8 2000 2 rlm 10.3 10.5 0.2 9 2011 1 rlm 11.6 12 0.4 102011 2 rlm 11.4 12 0.6 112022 1 rlm 11.8 12.1 0.1 122022 2 rlm 11.9 12.1 0.2 -- k.idx, step.forwd, pt.num and model columns are FACTORS. prev, value, abs.error are numeric I need to take the mean value of the numeric columns (prev, value and abs.error) for each k.idx and step.forwd and model. So: rows 1 and 2, 3 and 4, 5 and 6,7 and 8, 9 and 10, 11 and 12 must be grouped together. Next, i need to plot a boxplot of the mean(abs.error) of each model for each k.idx. I need to compare the abs.error of the two models for each step and the mean overall abs.error of each model. And so on. I read the manuals, but the examples there are too simple. I know how to do this manipulation in a brute force manner, but i wish to learn how to work the right way with R. Could someone help me? Thanks in advance. José Augusto Undergraduate student University of São Paulo Business Administration Faculty __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Same regression per sub-group: apply?
Dear helpers, I've come up with what is probably a simple problem, but I cannot find the solution. I have a data-set containing survey-data from several countries. What I want to do is to perform some regression analyses, for each country separately. The question is, how to do this nicely (thus without repeating the same syntax with another `subset' argument). I thought of the following: model.per.country - tapply(data, data$COUNTRY, function(x) glm (dependent.var ~ FEMALE + AGE + EDUCLIN + (), family=binomial, data=capital)) But this does not work. What goes wrong, I think, is that the dependent variable is clustered according to `Country', but not so for the predictors. The error message I received: Error in tapply(dat, dat$COUNTRY, function(x) glm(participate ~ FEMALE + : arguments must have same length Could you please help me solving this little problem? Thanks in advance: Rense Nieuwenhuis [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
